Spoiler:I too noticed that Johnny looked like a very young Solid Snake/Big Boss. I was waiting for exactly the same "confirmation" that you did. Maybe this is what Kojima meant that Solid's story is over. 'Cause it is. Kojima and Konami has already confirmed that there will be more Metal Gear games - but they won't center around Solid Snake, as his story is now officially concluded.
Maybe we'll see another Snake sometime in the future, if Johnny actually turns out to be a fourth clone. Maybe the reason he was created (and if Madnar is the same as the one in MG1 or 2) will be explained in a future game, but without being central to the main plot in that game. It could also be that Kojima made him look like a Snake because he simply loves to mess with the players minds.
Personally, I think MGS4 is one of the best games I've ever played, and that includes the first game. It was the perfect conclusion to a fantastically epic story. Now, if you'll excuse me, I think I'll go and play through it again.
